Problems with the size of the plots obtained with AffyPLM
1
0
Entering edit mode
@jordi-altirriba-gutierrez-682
Last seen 5.7 years ago
Dear BioC users, I am assessing the quality of 20 Affymetrix arrayx of the type HGU-133-Plus-2 through the AffyPLM package. Due to memory problems, I am using a remote PC with 2Gb of RAM with a Linux OS (I have very little experience using X OS). Everything is OK, but I can?t plot the image obtained with AffyPLM with this command: > image(Pset,which=1) The fact of using a remote connection, forces the use of postscript as the only way to obtain an image (I can?t open the X11 device with others commands as jpeg). I obtain these errors A) Problems with the margins: >postscript("QC.ps") >par(mfrow=c(7,3)) >image(Pset,which=1) Error in plot.new() : figure margins too large B) Problems with the file size: >postscript("QC.ps") >par(mfrow=c(7,3), mar=rep(1, 4)) >image(Pset,which=1) >image(Pset,which=20) >dev.off() The file obtained has a size of 805Mb, which is too big to work with it. I have tried to modify the values of mar (mar=c(0.1,0.1,0.1,0.1)) and the file have the same size. Moreover, I have tried to modify the postscript size postscript("QC.ps", width=1, height=1), without success. Is any way to solve this problem? (Probably there is a really easy way which due to my inexperience I can?t found, sorry. I have been googling without success). In other studies, using jpeg command and a Windows OS, the images produced have a reasonable size and the images are scaled to the dimensions of the plot. My session info: >sessionInfo() R version 2.4.0 (2006-10-03) i686-pc-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_ MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC _MEASUREME NT=en_US;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: hgu133plus2cdf affyPLM gcrma matchprobes affydata "1.14.0" "1.10.0" "2.6.0" "1.6.0" "1.10.0" affy affyio Biobase "1.12.1" "1.2.0" "1.12.2" Many thanks for your advices, Yours faithfully, Jordi Altirriba PhD student Barcelona, Spain _________________________________________________________________ Grandes ?xitos, superh?roes, imitaciones, cine y TV...
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio • 1.6k views
ADD COMMENT •
0
Entering edit mode
@oosting-j-path-412
Last seen 10.2 years ago
You could save the Pset object to a file and load it in at your Windows computer to create the images. At that time the linear model has been fitted, and the amount of needed memory should be a lot less. Jan -----Original Message----- Dear BioC users, I am assessing the quality of 20 Affymetrix arrayx of the type HGU-133-Plus-2 through the AffyPLM package. Due to memory problems, I am using a remote PC with 2Gb of RAM with a Linux OS (I have very little experience using X OS). Everything is OK, but I can't plot the image obtained with AffyPLM with this command: > image(Pset,which=1) The fact of using a remote connection, forces the use of postscript as the only way to obtain an image (I can't open the X11 device with others commands as jpeg).
ADD COMMENT •
0
Entering edit mode
Dear Jan Many thanks for your answer, but I can?t open a session in Windows which has been created with Linux. What I do is: At the end of my Lynux session: >save.image(?test.RData?) I export this file to the Windows PC and execute: >load(?test.RData?) Error in load(?test.RData?) ReadItem: type 25 unknown (I have translated it from the Spanish). Nevertheless, many thanks, Jordi >From: <j.oosting at="" lumc.nl=""> >To: <altirriba at="" hotmail.com="">,<bioconductor at="" stat.math.ethz.ch=""> >Subject: RE: [BioC] Problems with the size of the plots obtained with >AffyPLM >Date: Wed, 17 Jan 2007 09:28:15 +0100 > >You could save the Pset object to a file and load it in at your Windows >computer to create the images. At that time the linear model has been >fitted, and the amount of needed memory should be a lot less. > >Jan > >-----Original Message----- > Dear BioC users, > I am assessing the quality of 20 Affymetrix arrayx of the type >HGU-133-Plus-2 through the AffyPLM package. > Due to memory problems, I am using a remote PC with 2Gb of RAM with a >Linux OS (I have very little experience using X OS). > Everything is OK, but I can't plot the image obtained with AffyPLM with >this command: > > image(Pset,which=1) > The fact of using a remote connection, forces the use of postscript as >the only way to obtain an image (I can't open the X11 device with others >commands as jpeg). > _________________________________________________________________ ?Est?s pensando en cambiar de coche? Todas los modelos de serie y extras en
ADD REPLY •
0
Entering edit mode
It should not be a problem to load in data on windows when it is saved in linux if the version of R is the same on both sides. You could try to save just the Pset object by save(Pset,file="test.RData",compress=FALSE) Be sure to load the affyPLM library before loading in the file Jan -----Original Message----- From: Jordi Altirriba Guti?rrez [mailto:altirriba@hotmail.com] Sent: woensdag 17 januari 2007 16:27 To: Oosting, J. (PATH); bioconductor at stat.math.ethz.ch Subject: RE: [BioC] Problems with the size of the plots obtained with AffyPLM Dear Jan Many thanks for your answer, but I can't open a session in Windows which has been created with Linux. What I do is: At the end of my Lynux session: >save.image("test.RData") I export this file to the Windows PC and execute: >load("test.RData") Error in load("test.RData") ReadItem: type 25 unknown (I have translated it from the Spanish). Nevertheless, many thanks, Jordi >From: <j.oosting at="" lumc.nl=""> >To: <altirriba at="" hotmail.com="">,<bioconductor at="" stat.math.ethz.ch=""> >Subject: RE: [BioC] Problems with the size of the plots obtained with >AffyPLM >Date: Wed, 17 Jan 2007 09:28:15 +0100 > >You could save the Pset object to a file and load it in at your Windows >computer to create the images. At that time the linear model has been >fitted, and the amount of needed memory should be a lot less. > >Jan > >-----Original Message----- > Dear BioC users, > I am assessing the quality of 20 Affymetrix arrayx of the type >HGU-133-Plus-2 through the AffyPLM package. > Due to memory problems, I am using a remote PC with 2Gb of RAM with >a Linux OS (I have very little experience using X OS). > Everything is OK, but I can't plot the image obtained with AffyPLM >with this command: > > image(Pset,which=1) > The fact of using a remote connection, forces the use of postscript >as the only way to obtain an image (I can't open the X11 device with >others commands as jpeg). > _________________________________________________________________ ?Est?s pensando en cambiar de coche? Todas los modelos de serie y extras en MSN Motor. http://motor.msn.es/researchcentre/
ADD REPLY •
0
Entering edit mode
Dear Jan Many thanks for your answer!! (sorry for the delay, too much work in the lab...) The R version was different between the 2 computers. Now I have installed the same version in the Windows machine and I have done the jpeg image without any problem, scaled correctly and with a reasonable size. Again, many thanks!! Yours sincerelly, Jordi >From: <j.oosting at="" lumc.nl=""> >To: <altirriba at="" hotmail.com=""> >CC: <bioconductor at="" stat.math.ethz.ch=""> >Subject: RE: [BioC] Problems with the size of the plots obtained with >AffyPLM >Date: Wed, 17 Jan 2007 17:06:08 +0100 > >It should not be a problem to load in data on windows when it is saved in >linux if the version of R is the same on both sides. >You could try to save just the Pset object by >save(Pset,file="test.RData",compress=FALSE) >Be sure to load the affyPLM library before loading in the file > >Jan > >-----Original Message----- >From: Jordi Altirriba Guti?rrez [mailto:altirriba at hotmail.com] >Sent: woensdag 17 januari 2007 16:27 >To: Oosting, J. (PATH); bioconductor at stat.math.ethz.ch >Subject: RE: [BioC] Problems with the size of the plots obtained with >AffyPLM > >Dear Jan >Many thanks for your answer, but I can't open a session in Windows which >has been created with Linux. > >What I do is: >At the end of my Lynux session: > >save.image("test.RData") >I export this file to the Windows PC and execute: > >load("test.RData") >Error in load("test.RData") >ReadItem: type 25 unknown (I have translated it from the Spanish). > >Nevertheless, many thanks, > >Jordi > > > >From: <j.oosting at="" lumc.nl=""> > >To: <altirriba at="" hotmail.com="">,<bioconductor at="" stat.math.ethz.ch=""> > >Subject: RE: [BioC] Problems with the size of the plots obtained with > >AffyPLM > >Date: Wed, 17 Jan 2007 09:28:15 +0100 > > > >You could save the Pset object to a file and load it in at your Windows > >computer to create the images. At that time the linear model has been > >fitted, and the amount of needed memory should be a lot less. > > > >Jan > > > >-----Original Message----- > > Dear BioC users, > > I am assessing the quality of 20 Affymetrix arrayx of the type > >HGU-133-Plus-2 through the AffyPLM package. > > Due to memory problems, I am using a remote PC with 2Gb of RAM with > >a Linux OS (I have very little experience using X OS). > > Everything is OK, but I can't plot the image obtained with AffyPLM > >with this command: > > > image(Pset,which=1) > > The fact of using a remote connection, forces the use of postscript > >as the only way to obtain an image (I can't open the X11 device with > >others commands as jpeg). > > > >_________________________________________________________________ >?Est?s pensando en cambiar de coche? Todas los modelos de serie y extras en >MSN Motor. http://motor.msn.es/researchcentre/ > _________________________________________________________________ Moda para esta temporada. Ponte al d?a de todas las tendencias.
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 741 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6